A novel missense mutation of the paired box 3 gene in a Turkish family with Waardenburg syndrome type 1.

Purpose Screening of mutations in the paired box 3 (PAX3) gene in three generations of a Turkish family with Waardenburg syndrome type 1 (WS1). Methods WS1 was diagnosed in a 13-month-old girl according to the WS Consortium criteria. Detailed family history of the proband revealed eight affected members in three generations. Routine clinical and audiological examination and ophthalmologic evaluation were performed on eight affected and five healthy members of the study family. Dystopia canthorum was detected in all affected patients; however, a brilliant blue iris was present in five patients who also had mild retinal hypopigmentation. Genomic DNA was extracted from the peripheral blood of affected and unaffected individuals in the family as well as 50 unrelated healthy volunteers. All coding exons and adjacent intronic regions of PAX3 were sequenced directly. Results A novel missense heterozygous c.788T>G mutation was identified in eight patients. This nucleotide alteration was not found in unaffected members of the study family or in the 50 unrelated control subjects. The mutation causes V263G amino-acid substitution in the homeodomain of the PAX3 protein, which represents the 45th residue of helix 3. Conclusions We identified a novel missense c.788T>G mutation in PAX3 in a family with Waardenburg syndrome with intrafamilial phenotypic heterogeneity.

PAX3, located on the long arm of chromosome 2 (2q35), includes ten exons [27]. This gene is a member of the mammalian PAX gene family that encodes for DNA-binding transcription factors and plays a role in maintaining stem cell pluripotency, cell-lineage specification, proliferation, migration, apoptosis, and inhibition of terminal differentiation [28,29]. PAX3 is expressed in neural crest cells including the spinal ganglia, the craniofacial mesectoderm, and the limb mesenchyme during embryogenesis and plays an important role in the migration and differentiation of melanocytes, which originate from the embryonic neural crest [17,28].
More than 70 pathogenic PAX3 mutations including missense, nonsense, and frameshifts mutations, small insertions or deletions, and splice alterations have been reported in patients with WS1 [17]. Most PAX3 mutations are located in exon 2; no mutations have been described in exons 9 and 10. Approximately 50% of the described mutations of PAX3 are missense; the remaining are truncating variations [17]. Partial or total gene deletions have been reported in 10% of patients without identified point mutations [30][31][32][33][34][35]. The literature that studied patients with WS1 caused by mutations in PAX3 was reviewed in 2009 by Pingault et al., and no relationship was found between the severity of disease and the type of mutation [17]. In this report, clinical features and intrafamilial heterogeneity of eight affected individuals in a Turkish family with WS1 with a novel mutation are presented.  [3]. Her family history revealed eight affected members in three generations ( Figure 1). Routine clinical examination and detailed audiological and ophthalmologic evaluation were performed on eight affected and five healthy members of the study family. Two major or one major and two minor criteria must be found in an individual to diagnose WS. In four patients (IV:3, IV:4, IV:5, and IV:6), premature graying of the hair was not evaluated because of the patients' youth.

METHODS
Hearing loss was assessed with pure tone audiometry or, in children, with brainstem-evoked response audiometry (BERA). Degree of hearing loss was computed by using a four-frequency average called the pure-tone average. The average of the hearing threshold levels (decibels) taken at 500 Hz, 1000 Hz, 2000 Hz, and 4000 Hz was calculated for each patient to find the pure-tone average level. Afterwards, hearing loss was graded according to the classification defined by J.G. Clark in 1981 [36]. Dystopia canthorum, which is characterized by an increase in the distance between the inner angles of the eyelids with normal distances between the pupils and the outer canthus, was defined for each affected member of the family with a W index that exceeds 1.95 [1].
Mutation analysis: Peripheral blood samples which were collected in EDTA tubes and stored fresh (-20 °C) were obtained from participating members of the family and 50 unrelated healthy volunteers. Genetic analyses were performed in Duzen Laboratory Groups, Genetics Division, Ankara, Turkey. Genomic DNA was extracted from leukocytes using the QIAamp DNA mini kit (Qiagen, 51304, Dusseldorf, Germany), according to manufacturer's instructions. Genomic fragments including coding regions and adjacent intronic regions of PAX3 were amplified with PCR, using nine primer pairs described previously [7] ( Table  1). The amplicons from individual exons were purified and analyzed with cycle sequencing with ABI BigDye Terminator Cycle Sequencing Kit v3.1 (ABI Applied Biosystems, Foster City, CA) on an automatic DNA sequencer (ABI 3130 Genetic Analyzer, Applied Biosystems). Sequencing results from patients and the consensus sequences from the NCBI Human Genome Database (NCBI Reference Sequence: NG_011632.1) were imported into the ABI SeqScape program and aligned to identify variations. Each found mutation was confirmed with bidirectional sequencing. The mutation was named following the nomenclature recommended by the Human Genomic Variation Society.  Table 2.

Phenotype analysis:
Dystopia canthorum was detected in all affected patients ( Figure 2). A brilliant blue iris was present in five patients who also had mild retinal hypopigmentation (III:5, III:7, III:9, IV:5, and IV:6; Figure 2 and Figure 3). Orthoptic assessments were within normal limits, and nystagmus was not present in affected patients or nonaffected members of the family; however, astigmatic refractive errors were found frequently in all affected members. Synophrys was presented in five out of eight patients (II:3, III:5, III:7, III:9, and IV:4), and this finding was more prominent in two (II:3 and III:9; Figure 2). Clinical features of all unaffected family members (II:1, III:1, III:2, IV:1, and IV:2) were revealed as normal.
Four patients had a sensorineural hearing impairment. Three (III:5, IV:5, and IV:6) were profoundly and one (III:9) was moderately deaf. Out of the three profoundly deaf patients, two (IV:5 and IV:6) had received a cochlear implant. None had a white forelock, whereas premature graying of the hair (before the age of 30 years) was present in patients II:3, III:5, III:7, and III:9. Due to the patients' youth, premature graying of the hair was not evaluated in four patients (IV:4 was 15 years old, IV:5 was 10 years old; IV:3 and IV:6 were younger than 2 years old). Hypopigmented patches of the skin were present in only one patient (III:9; Table 2). No patients had limb defects.
Mutation analysis: After direct sequencing of PAX3, a heterozygous change T>G in exon 5, at position 788 of the translation start site was detected in all affected patients ( Figure  4A). This position belongs to helix 3 of the homeodomain in the PAX3 protein, and converts the 45 th amino acid in this domain from valine to glycine. This mutation was not found in the other unaffected relatives (II:1, III:2, IV:1, and IV:2) in the healthy controls ( Figure 4B). Case III:1 declined the molecular genetic analysis.

DISCUSSION
A careful clinical evaluation is necessary to differentiate various types of WS. Dystopia canthorum is a commonly seen feature of WS with an incidence of 41.2% to 99% [1,2]. However, dystopia canthorum is also the most penetrant (%99) and the most distinguishing feature of WS1 [1,2,6,37,38]. All affected patients in the present study had dystopia canthorum.
In 2006, the frequencies of heterochromia iridis and synophrys were reported as 25% and 45% of WS1 patients, respectively [6]. However, incidence of synophrys in patients with WS1 was reported as 85% in a review published in 2009 [17]. Although a brilliant blue iris was present in five out of eight patients, heterochromia iridis was not detected in any members of the study family. However, synophrys, a minor criterion, was also present in five out of eight patients.
WS accounts for approximately 2% to 5% of congenital sensorineural deafness [30,39]. Congenital sensorineural deafness is a feature in approximately 25% to 75% of patients with WS1 [17,40,41]. Deafness related to WS can be moderate to severe, unilateral, or bilateral but most commonly nonprogressive [40,42]. In our study, three patients had total bilateral severe sensorineural deafness, and one patient had moderate bilateral deafness. Hearing tests were normal in the other four affected patients and five unaffected members of the family. However, Wang et al. reported a lack of deafness among their Chinese patients with WS1, and indicated a possible ethnic specific variation in clinical expression   of the syndrome [43]. The incidence of hearing loss among Turkish patients with WS1 was published as 75% by Oysu et al. in 2000 [40]. Hearing loss was present in 50% of our study patients with WS1, which is in accordance with the literature [17,30,[39][40][41][42].
Mutations of PAX3 on chromosome 2q37 have been reported in 33% to 80% of patients with WS1 in familial and sporadic cases [3,7,13,44]. PAX3 is a transcription factor that plays a major role in embryogenesis [45]. By 2009, about 70 mutations of PAX3 related to WS had been introduced [17]. The PAX3 protein is a member of the family of paired domain proteins that bind DNA and regulate gene expression [7]. PAX3 encodes a paired domain and a homeodomain [6]. Missense mutations are almost exclusively located within the two DNA binding domains. One, the homeodomain, includes three α-helices. Most PAX3 mutations are located in the paired domain or in helix 3 of the homeodomain [6]. Helix 3 of the homeodomain makes sequence-specific DNA contacts and several phosphate contacts in the major groove [6,7]. Mutations that affect helix 3 of the homeodomain in the PAX3 protein may lead to a decrease in DNA binding affinity and/or specificity [7]. We identified the novel c.788T>G mutation in PAX3 leading to V→G substitution on the 45 th position of helix 3.
The phenotypic variability among the eight affected patients with the same mutation is well matched with inheritance properties of the disease. PAX3 mutations are inherited dominantly with variable expressivity [43]. The disease is known as fully penetrant when at least one of its signs is detected, but the penetrance for each one is not complete. The fact that there is no obvious association between different types of mutations and the severity of disease could be due to the role of gene dosage as the pathophysiology of the syndrome. It is hypothesized that stochastic events were not solely responsible for its expression, so that genetic factors and/or the environmental background can modify the phenotype [17]. A few mutations of PAX3 have been tested for their functional consequences. The functional experiments mostly included DNA-binding activity and transactivation capabilities. Although missense mutations are thought to abolish PAX3 ability to bind and activate its transcriptional targets, further functional studies are necessary to evaluate the precise molecular mechanism caused by the c.788T>G mutation.
In conclusion, we identified a novel missense mutation in PAX3 that is associated with the occurrence of WS1. The new mutation, like all other defined mutations, lead to phenotypic variability within the same family, which is one of the most important features of the disease.

ACKNOWLEDGMENTS
We certify that any affiliations with or involvement in any organization or entity with direct financial interest in the subject matter or materials discussed in the manuscript are disclosed in the paper. Financial support of the present study was provided by the Project Support Committee of Dr.Behçet Uz Children's Hospital. Neither this manuscript nor one with substantially similar content under our authorship has been published or is being considered for publication elsewhere.